A Comprehensive Introduction to Command Line for R Users

• exploring R release names
• mapping shell commands to R functions
• RStudio Terminal
• executing shell commands from R using system2() or processx::run()
• execute shell commands in RMarkdown
• execute R scripts in the shell

If you want a deeper understanding of using command line for data science, we suggest you read Data Science at the Command Line. Software Carpentry too has a lesson on shell. We have listed more references at the end of the tutorial for the benefit of the readers.

Table of Contents

• Resources
• Introduction
• Navigating File System
• File Management
• Input/Output
• Search & Regular Expression
• Data Transfer
• File Compression
• System Info
• Execute Shell Commands from R
• Execute Shell Commands in RStudio
• Execute Shell Commands in RMarkdown
• Execute R Commands in Shell
• Summary
• References

Resources

Below are the links to all the resources related to this post:

You can try our free online course Command Line Basics for R Users if you prefer to learn through self paced online courses or our ebook if you like to read the tutorial in a book format.

Introduction

What is Shell/Terminal?

Shell is a text based application for viewing, handling & manipulating files. It takes in commands and passes them on to the operating system. It is also known as

• CLI (Command Line Interface)
• Bash (Bourne Again Shell)
• Terminal

It is sufficient to know a handful of commands to get started with the shell.

Launch Terminal

Although we will use the terminal in RStudio on RStudio Cloud, we should still know how to launch the terminal in different operating systems.

mac

Applications -> Utility -> Terminal

Windows

Option 1

Go to the Start Menu or screen and enter Command Prompt in the search field.

Option 2

Start Menu -> Windows System -> Command Prompt

Option 3

Hold the Windows key and press the R key to get a Run window. Type cmd in the box and click on the OK button.

Linux

• Applications -> Accessories -> Terminal
• Applications -> System -> Terminal

Windows Subsystem for Linux

If you want to use bash on Windows, try the Windows subsystem for Linux. It only works on 64 bit Windows 10. Below are the steps to enable Windows subsystem fro Linux:

Step 1 - Enable Developer Mode

To enable Developer Mode open the Settings app and head to Update & Security > For Developers. Press the Developer Mode switch.

Step 2 - Enable Windows Subsystem for Linux

To enable the Windows Subsystem for Linux (Beta), open the Control Panel, click Programs and Features, and click Turn Windows Features On or Off in left side bar under Programs and Features. Enable the Windows Subsystem for Linux (Beta) option in the list here and click OK. After you do, you’ll be prompted to reboot your computer. Click Restart Now to reboot your computer and Windows 10 will install the new feature.

Step 3 - Install your Linux Distribution of Choice

Open the Microsoft store and choose your favorite Linux distribution.

In the distro’s page, click on “Get”.

Launch the distro from the Start Menu.

You can learn more about the Windows Subsystem for Linux here.

RStudio Terminal

RStudio introduced the terminal with version 1.1.383. The terminal tab is next to the console tab. If it is not visible, use any of the below methods to launch it

• Shift + Alt + T
• Tools -> Terminal -> New Terminal

Note, the terminal depends on the underlying operating system. To learn more about the RStudio terminal, read this article or watch this webinar. In this book, we will use the RStudio terminal on RStudio Cloud to ensure that all users have access to Linux bash. You can try all the commands used in this book on your local system as well except in case of Windows users.

Prompt

As soon as you launch the terminal, you will see the hostname, machine name and the prompt. In case of mac & Linux users, the prompt is $ . For Windows users, it is > .

Get Started

To begin with, let us learn to display

• basic information about the user
• the current date & time
• the calendar
• and clear the screen.

whoami prints the effective user id i.e. the name of the user who runs the command. Use it to verify the user as which you are logged into the system.

whoami

## aravind

date will display or change the value of the system’s time and date information.

date

## Wed Jun 10 22:45:47 IST 2020

cal will display a formatted calendar and clear will clear all text on the screen and display a new prompt. You can clear the screen by pressing Ctrl + L as well.

In R, we can get the user information from Sys.info() or whoami() from the whoami package. The current date & time are returned by Sys.date() & Sys.time() . To clear the R console, we use Ctrl + L.

Help/Documentation

Before we proceed further, let us learn to view the documentation/manual pages of the commands.

man is used to view the system’s reference manual. Let us use it to view the documentation of the whatis command which we will use next.

man whatis

## WHATIS(1) Manual pager utils WHATIS(1) ## ## NAME ## whatis - display one-line manual page descriptions ## ## SYNOPSIS ## whatis [-dlv?V] [-r|-w] [-s list] [-m system[. ]] [-M path] [-L ## locale] [-C file] name . ## ## DESCRIPTION ## Each manual page has a short description available within it. whatis ## searches the manual page names and displays the manual page descrip‐ ## tions of any name matched. ## ## name may contain wildcards (-w) or be a regular expression (-r). Using ## these options, it may be necessary to quote the name or escape (\) the ## special characters to stop the shell from interpreting them. ## ## index databases are used during the search, and are updated by the ## mandb program. Depending on your installation, this may be run by a ## periodic cron job, or may need to be run manually after new manual ## pages have been installed. To produce an old style text whatis data‐ ## base from the relative index database, issue the command: ## ## whatis -M manpath -w '*' | sort > manpath/whatis ## ## where manpath is a manual page hierarchy such as /usr/man. ## ## OPTIONS ## -d, --debug ## Print debugging information. ## ## -v, --verbose ## Print verbose warning messages. ## ## -r, --regex ## Interpret each name as a regular expression. If a name matches ## any part of a page name, a match will be made. This option ## causes whatis to be somewhat slower due to the nature of data‐ ## base searches. ## ## -w, --wildcard ## Interpret each name as a pattern containing shell style wild‐ ## cards. For a match to be made, an expanded name must match the ## entire page name. This option causes whatis to be somewhat ## slower due to the nature of database searches. ## ## -l, --long ## Do not trim output to the terminal width. Normally, output will ## be truncated to the terminal width to avoid ugly results from ## poorly-written NAME sections. ## ## -s list, --sections list, --section list ## Search only the given manual sections. list is a colon- or ## comma-separated list of sections. If an entry in list is a sim‐ ## ple section, for example "3", then the displayed list of ## descriptions will include pages in sections "3", "3perl", "3x", ## and so on; while if an entry in list has an extension, for exam‐ ## ple "3perl", then the list will only include pages in that exact ## part of the manual section. ## ## -m system[. ], --systems=system[. ] ## If this system has access to other operating system's manual ## page names, they can be accessed using this option. To search ## NewOS's manual page names, use the option -m NewOS. ## ## The system specified can be a combination of comma delimited ## operating system names. To include a search of the native oper‐ ## ating system's manual page names, include the system name man in ## the argument string. This option will override the $SYSTEM ## environment variable. ## ## -M path, --manpath=path ## Specify an alternate set of colon-delimited manual page hierar‐ ## chies to search. By default, whatis uses the $MANPATH environ‐ ## ment variable, unless it is empty or unset, in which case it ## will determine an appropriate manpath based on your $PATH envi‐ ## ronment variable. This option overrides the contents of $MAN‐ ## PATH. ## ## -L locale, --locale=locale ## whatis will normally determine your current locale by a call to ## the C function setlocale(3) which interrogates various environ‐ ## ment variables, possibly including $LC_MESSAGES and $LA

whatis displays short manual page descriptions (each manual page has a short description available within it).

whatis ls

## ls (1) - list directory contents

You will find tldr.sh very useful while exploring new commands and there is a related R package, tldrrr as well.

# devtools::install_github("kirillseva/tldrrr") tldrrr::tldr("pwd")

## pwd ## ## Print name of current/working directory. ## ## • Print the current directory: ## ## pwd ## ## • Print the current directory, and resolve all symlinks (i.e. show the "physical" path): ## ## pwd -P

Navigating File System

In this section, we will learn commands that will help us

• navigate between different folders/directories
• return current working directory
• list all the files & folders in a directory
• create and delete directories

pwd displays the name of the present working directory.

## /mnt/j/R/Others/blogs/content/post/cline

ls displays information about files and directories in the current directory along with their associated metadata such as

• size
• ownership
• modification date

With no options, it will list the files and directories in the current directory, sorted alphabetically.

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

cd (change directory) changes the current working directory. It is among the most used commands as it allows the user to move around the file system.

cd r pwd

## /mnt/j/R/Others/blogs/content/post/cline/r

mkdir will create new directory. It will allow you to set file mode (permissions associated with the directory) i.e. who can open/modify/delete the directory.

mkdir rfiles ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## rfiles ## sept_15.csv.gz ## urls.txt ## zip_example.zip

rmdir will remove empty directories from the file system. It can be used to remove multiple empty directories as well. If the directory is not empty, rmdir will not remove it and instead display a warning that the directory is not empty.

rmdir rfiles ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Change Working Directory

Let us focus a bit more on changing working directory. The below table shows commands for changing working directory to

• up one level
• previous working directory
• home directory
• and root directory

All files and directories stem from one main directory, the root directory. All the other directories in the system are sub-directories of the root directory and the root directory has no parent directory. It is represented by a single slash ( / ). cd / will change the current working directory to the root directory. In RStudio Cloud, use cd and cd .. to navigate back to the current working directory. If you get confused, close the terminal and relaunch it.

cd / pwd

The parent directory i.e. the directory one level up from the current directory which contains the directory we are in now is represented by two dots ( .. ). cd .. will change us into the parent directory of the current directory.

cd .. pwd

## /mnt/j/R/Others/blogs/content/post

The home directory is the directory we are placed in, by default, when we launch a new terminal session. It is represented by the tilde ( ~ ). In RStudio Cloud, use cd and cd .. to navigate back to the current working directory. If you get confused, close the terminal and relaunch it.

cd ~ pwd

## /home/aravind

To change into the previous working directory, use cd - .

cd - pwd

## /mnt/j/R/Others/blogs/content/post ## /mnt/j/R/Others/blogs/content/post

The current working directory is represented by a single dot ( . ). cd . will change us into the current directory i.e. it will do nothing.

List Directory Contents

ls will list the contents of a directory. Using different arguments, we can

• list hidden files
• view file permissions, ownership, size & modification date
• sort by size & modification date

List files one per line

ls -l

## total 31108 ## -rwxrwxrwx 1 aravind aravind 12 Jun 3 13:51 analysis.R ## -rwxrwxrwx 1 aravind aravind 430 Jun 3 13:51 bash.R ## -rwxrwxrwx 1 aravind aravind 16242 Jun 3 13:51 bash.sh ## -rwxrwxrwx 1 aravind aravind 35 Jun 3 13:51 imports_blorr.txt ## -rwxrwxrwx 1 aravind aravind 34 Jun 3 13:51 imports_olsrr.txt ## -rwxrwxrwx 1 aravind aravind 39501 Jun 3 13:51 lorem-ipsum.txt ## -rwxrwxrwx 1 aravind aravind 9291 Jun 3 13:51 main_project.zip ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myfiles ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 mypackage ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject1 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject2 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject3 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject4 ## -rwxrwxrwx 1 aravind aravind 1498 Jun 3 13:51 package_names.txt ## -rwxrwxrwx 1 aravind aravind 1082 Jun 3 13:51 pkg_names.txt ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 r ## -rwxrwxrwx 1 aravind aravind 10240 Jun 3 13:51 release_names.tar ## -rwxrwxrwx 1 aravind aravind 632 Jun 3 13:51 release_names.tar.gz ## -rwxrwxrwx 1 aravind aravind 546 Jun 3 13:51 release_names.txt ## -rwxrwxrwx 1 aravind aravind 65 Jun 3 13:51 release_names_18.txt ## -rwxrwxrwx 1 aravind aravind 53 Jun 3 13:51 release_names_19.txt ## -rwxrwxrwx 1 aravind aravind 31754998 Jun 3 13:51 sept_15.csv.gz ## -rwxrwxrwx 1 aravind aravind 157 Jun 3 13:51 urls.txt ## -rwxrwxrwx 1 aravind aravind 4398 Jun 3 13:51 zip_example.zip

List all files including hidden files

ls -a

## . ## .. ## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Display file permissions, ownership, size & modification date

ls -la

## total 31108 ## drwxrwxrwx 1 aravind aravind 4096 Jun 10 22:46 . ## drwxrwxrwx 1 aravind aravind 4096 Jun 10 22:45 .. ## -rwxrwxrwx 1 aravind aravind 12 Jun 3 13:51 analysis.R ## -rwxrwxrwx 1 aravind aravind 430 Jun 3 13:51 bash.R ## -rwxrwxrwx 1 aravind aravind 16242 Jun 3 13:51 bash.sh ## -rwxrwxrwx 1 aravind aravind 35 Jun 3 13:51 imports_blorr.txt ## -rwxrwxrwx 1 aravind aravind 34 Jun 3 13:51 imports_olsrr.txt ## -rwxrwxrwx 1 aravind aravind 39501 Jun 3 13:51 lorem-ipsum.txt ## -rwxrwxrwx 1 aravind aravind 9291 Jun 3 13:51 main_project.zip ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myfiles ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 mypackage ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject1 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject2 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject3 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject4 ## -rwxrwxrwx 1 aravind aravind 1498 Jun 3 13:51 package_names.txt ## -rwxrwxrwx 1 aravind aravind 1082 Jun 3 13:51 pkg_names.txt ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 r ## -rwxrwxrwx 1 aravind aravind 10240 Jun 3 13:51 release_names.tar ## -rwxrwxrwx 1 aravind aravind 632 Jun 3 13:51 release_names.tar.gz ## -rwxrwxrwx 1 aravind aravind 546 Jun 3 13:51 release_names.txt ## -rwxrwxrwx 1 aravind aravind 65 Jun 3 13:51 release_names_18.txt ## -rwxrwxrwx 1 aravind aravind 53 Jun 3 13:51 release_names_19.txt ## -rwxrwxrwx 1 aravind aravind 31754998 Jun 3 13:51 sept_15.csv.gz ## -rwxrwxrwx 1 aravind aravind 157 Jun 3 13:51 urls.txt ## -rwxrwxrwx 1 aravind aravind 4398 Jun 3 13:51 zip_example.zip

Display size in human readable format

ls -lh

## total 31M ## -rwxrwxrwx 1 aravind aravind 12 Jun 3 13:51 analysis.R ## -rwxrwxrwx 1 aravind aravind 430 Jun 3 13:51 bash.R ## -rwxrwxrwx 1 aravind aravind 16K Jun 3 13:51 bash.sh ## -rwxrwxrwx 1 aravind aravind 35 Jun 3 13:51 imports_blorr.txt ## -rwxrwxrwx 1 aravind aravind 34 Jun 3 13:51 imports_olsrr.txt ## -rwxrwxrwx 1 aravind aravind 39K Jun 3 13:51 lorem-ipsum.txt ## -rwxrwxrwx 1 aravind aravind 9.1K Jun 3 13:51 main_project.zip ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 myfiles ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 mypackage ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 myproject ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 myproject1 ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 myproject2 ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 myproject3 ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 myproject4 ## -rwxrwxrwx 1 aravind aravind 1.5K Jun 3 13:51 package_names.txt ## -rwxrwxrwx 1 aravind aravind 1.1K Jun 3 13:51 pkg_names.txt ## drwxrwxrwx 1 aravind aravind 4.0K Jun 3 13:51 r ## -rwxrwxrwx 1 aravind aravind 10K Jun 3 13:51 release_names.tar ## -rwxrwxrwx 1 aravind aravind 632 Jun 3 13:51 release_names.tar.gz ## -rwxrwxrwx 1 aravind aravind 546 Jun 3 13:51 release_names.txt ## -rwxrwxrwx 1 aravind aravind 65 Jun 3 13:51 release_names_18.txt ## -rwxrwxrwx 1 aravind aravind 53 Jun 3 13:51 release_names_19.txt ## -rwxrwxrwx 1 aravind aravind 31M Jun 3 13:51 sept_15.csv.gz ## -rwxrwxrwx 1 aravind aravind 157 Jun 3 13:51 urls.txt ## -rwxrwxrwx 1 aravind aravind 4.3K Jun 3 13:51 zip_example.zip

Sort list by size

ls -lS

## total 31108 ## -rwxrwxrwx 1 aravind aravind 31754998 Jun 3 13:51 sept_15.csv.gz ## -rwxrwxrwx 1 aravind aravind 39501 Jun 3 13:51 lorem-ipsum.txt ## -rwxrwxrwx 1 aravind aravind 16242 Jun 3 13:51 bash.sh ## -rwxrwxrwx 1 aravind aravind 10240 Jun 3 13:51 release_names.tar ## -rwxrwxrwx 1 aravind aravind 9291 Jun 3 13:51 main_project.zip ## -rwxrwxrwx 1 aravind aravind 4398 Jun 3 13:51 zip_example.zip ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myfiles ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 mypackage ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject1 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject2 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject3 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject4 ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 r ## -rwxrwxrwx 1 aravind aravind 1498 Jun 3 13:51 package_names.txt ## -rwxrwxrwx 1 aravind aravind 1082 Jun 3 13:51 pkg_names.txt ## -rwxrwxrwx 1 aravind aravind 632 Jun 3 13:51 release_names.tar.gz ## -rwxrwxrwx 1 aravind aravind 546 Jun 3 13:51 release_names.txt ## -rwxrwxrwx 1 aravind aravind 430 Jun 3 13:51 bash.R ## -rwxrwxrwx 1 aravind aravind 157 Jun 3 13:51 urls.txt ## -rwxrwxrwx 1 aravind aravind 65 Jun 3 13:51 release_names_18.txt ## -rwxrwxrwx 1 aravind aravind 53 Jun 3 13:51 release_names_19.txt ## -rwxrwxrwx 1 aravind aravind 35 Jun 3 13:51 imports_blorr.txt ## -rwxrwxrwx 1 aravind aravind 34 Jun 3 13:51 imports_olsrr.txt ## -rwxrwxrwx 1 aravind aravind 12 Jun 3 13:51 analysis.R

Sort list by modification date

ls -ltr

## total 31108 ## -rwxrwxrwx 1 aravind aravind 546 Jun 3 13:51 release_names.txt ## -rwxrwxrwx 1 aravind aravind 10240 Jun 3 13:51 release_names.tar ## -rwxrwxrwx 1 aravind aravind 4398 Jun 3 13:51 zip_example.zip ## -rwxrwxrwx 1 aravind aravind 9291 Jun 3 13:51 main_project.zip ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 r ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myfiles ## -rwxrwxrwx 1 aravind aravind 632 Jun 3 13:51 release_names.tar.gz ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject3 ## -rwxrwxrwx 1 aravind aravind 35 Jun 3 13:51 imports_blorr.txt ## -rwxrwxrwx 1 aravind aravind 65 Jun 3 13:51 release_names_18.txt ## -rwxrwxrwx 1 aravind aravind 53 Jun 3 13:51 release_names_19.txt ## -rwxrwxrwx 1 aravind aravind 34 Jun 3 13:51 imports_olsrr.txt ## -rwxrwxrwx 1 aravind aravind 1498 Jun 3 13:51 package_names.txt ## -rwxrwxrwx 1 aravind aravind 157 Jun 3 13:51 urls.txt ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject1 ## -rwxrwxrwx 1 aravind aravind 1082 Jun 3 13:51 pkg_names.txt ## -rwxrwxrwx 1 aravind aravind 31754998 Jun 3 13:51 sept_15.csv.gz ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 mypackage ## -rwxrwxrwx 1 aravind aravind 16242 Jun 3 13:51 bash.sh ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject2 ## -rwxrwxrwx 1 aravind aravind 12 Jun 3 13:51 analysis.R ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject ## -rwxrwxrwx 1 aravind aravind 430 Jun 3 13:51 bash.R ## -rwxrwxrwx 1 aravind aravind 39501 Jun 3 13:51 lorem-ipsum.txt ## drwxrwxrwx 1 aravind aravind 4096 Jun 3 13:51 myproject4

R Functions

In R, getwd() will return the current working directory. You can use here() from the here package as well. To change the current working directory, use setwd() . The fs package provides useful functions for file operations.

File Management

In this section, we will explore commands for file management including:

• create new file/change timestamps
• copying files
• renaming/moving files
• deleting files
• comparing files

Create new file

touch modifies file timestamps which is information associated with file modification. It can be any of the following:

• access time (the last time the file was read)
• modification time (the last time the contents of the file was changed)
• change time (the last time the file’s metadata was changed)

If the file does not exist, it will create an empty file of the same name. Let us use touch to create a new file myanalysis.R .

touch myanalysis.R ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myanalysis.R ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Copy Files/Folders

cp makes copies of files and directories. The general form of the command is cp source destination. By default, it will overwrite files without prompting for confirmation so be cautious while copying files or folders.

Copy files in same folder

Let us create a copy of release_names.txt file and name it as release_names_2.txt .

cp release_names.txt release_names_2.txt ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myanalysis.R ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## release_names_2.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Copy files into different folder

To copy a file into a different directory/folder, we need to specify the name of the destination folder. If the copied file should have a different name, then we need to specify the new name of the file as well. Let us copy the release_names.txt file into the r_releases folder (we will retain the same name for the file as we are copying it into a different folder).

cp release_names.txt r_releases/release_names.txt

Let us check if the file has been copied by listing the files in the r_releases folder using ls .

ls r_releases

## release_names.txt

Copy folders

How about making copies of folders? Use the -r option to copy entire folders. Let us create a copy of the r folder and name it as r2 . The -r option stands for --recursive i.e. copy directories recursively.

cp -r r r2 ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myanalysis.R ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## release_names_2.txt ## release_names_3.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Move/Rename Files

mv moves and renames files and directories. Using different options, we can ensure

• files are not overwritten
• user is prompted for confirmation before overwriting files
• details of files being moved is displayed

Let us move the release_names_2.txt file to the r_releases folder.

mv release_names_2.txt r_releases

Use ls to verfiy if the file has been moved. As you can see, release_names_2.txt is not present in the current working directory.

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myanalysis.R ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## release_names_3.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Let us check if release_names_2.txt is present in the r_releases folder. Great! We have successfully moved the file into a different folder.

ls r_releases

## release_names.txt ## release_names_2.txt

Move files in verbose mode

To view the details of the files being moved/renamed, use the -v option. In the below example, we move the release_names_3.txt file into the r_releases folder using mv .

mv -v release_names_3.txt r_releases

## renamed 'release_names_3.txt' -> 'r_releases/release_names_3.txt'

Do not overwrite existing files

How do we ensure that files are not overwritten without prompting the user first? In the below example, we will try to overwrite the release_names_2.txt in the r_releases folder using mv and see what happens. But first, let us look at the contents of the release_names_2.txt file using the cat command.

We will look into the cat command in more detail in the next chapter but for the time being it is sufficient to know that it prints contents of a file. The file contains release names of different R versions.

cat r_releases/release_names_2.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle ## Roasted Marshmallows ## Trick or Treat ## Security Blanket ## Masked Marvel ## Good Sport ## Frisbee Sailing ## Warm Puppy ## Spring Dance ## Sock it to Me ## Pumpkin Helmet ## Smooth Sidewalk ## Full of Ingredients ## World-Famous Astronaut ## Fire Safety ## Wooden Christmas Tree ## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch ## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tree

In our current working directory, we will create another file of the same name i.e. release_names_2.txt but its contents are different from the file in the r_releases folder. It contains the string release_names and nothing else. We will now move this file into the r_releases folder but use the option -n to ensure that the file in the r_releases folder is not overwritten. We can confirm this by printing the contents of the file in the r_releases folder.

The echo command is used to print text to the terminal or to write to a file. We will explore it in more detail in the next chapter.

echo "release_names" > release_names_2.txt mv -n release_names_2.txt r_releases cat r_releases/release_names_2.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle ## Roasted Marshmallows ## Trick or Treat ## Security Blanket ## Masked Marvel ## Good Sport ## Frisbee Sailing ## Warm Puppy ## Spring Dance ## Sock it to Me ## Pumpkin Helmet ## Smooth Sidewalk ## Full of Ingredients ## World-Famous Astronaut ## Fire Safety ## Wooden Christmas Tree ## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch ## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tree

As you can observe, the contents of the file in the r_releases folder has not changed. In the next section, we will learn to overwrite the contents using the -f option.

Do not prompt for confirmation before overwriting files

What if we actually intend to overwrite a file and do not want to be prompted for confirming the same. In this case, we can use the -f option which stands for --force i.e. do not prompt before overwriting. Let us first print the contents of the release_names_2.txt file in the r_releases folder.

cat r_releases/release_names_2.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle ## Roasted Marshmallows ## Trick or Treat ## Security Blanket ## Masked Marvel ## Good Sport ## Frisbee Sailing ## Warm Puppy ## Spring Dance ## Sock it to Me ## Pumpkin Helmet ## Smooth Sidewalk ## Full of Ingredients ## World-Famous Astronaut ## Fire Safety ## Wooden Christmas Tree ## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch ## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tree

Now we will create another file of the same name in the current working directory but with different content and use the -f option to overwrite the file in the r_releases folder. You can see that the contents of the file in the r_releases folder has changed.

echo "release_names" > release_names_2.txt mv -f release_names_2.txt r_releases cat r_releases/release_names_2.txt

## release_names

Remove/Delete Files

The rm command is used to delete/remove files & folders. Using additional options, we can

• remove directories & sub-directories
• forcibly remove directories
• interactively remove multiple files
• display information about files removed/deleted

Remove files

Let us use rm to remove the file myanalysis.R (we created it earlier using the touch command).

rm myanalysis.R ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject1 ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Recursive Deletion

How about folders or directories? We can remove a directory and all its contents including sub-directories using the option -r which stands for --recursive and removes directories and their contents recursively. Let us remove the myproject1 folder and all its contents.

rm -r myproject1 ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject2 ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Force Removal

Use the -f option which stands for --force to forciby remove directory and all its contents without prompting for confirmation or showing error messages. Let us remove the myproject2 folder and all its contents.

rm -rf myproject2 ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Verbose Mode

Remove files in verbose mode, printing a message for each removed file. This is useful when you want to see the details of the files being removed. In the below example, we will remove all files with .txt extension from the myfiles folder. Instead of specifying the name of each text file, we use the wildcard * along with .txt i.e. any file with the extension .txt will be removed.

cd myfiles rm -v *.txt

## removed 'release_names.txt' ## removed 'release_names_18.txt' ## removed 'release_names_19.txt'

Compare Files

diff stands for difference. It is used to compare files line by line and display differences. It also indicates which lines in one file must be changed to make the files identical. Using additional options, we can

• ignore white spaces while comparing files
• show differences sidy by side
• show differences in unified format
• compare directories recursively
• display names of files that differ

Compare Files

Let us compare the contents of the following files

• imports_olsrr.txt
• imports_blorr.txt

The files contain the names of R packages imported by the olsrr and blorr packages respectively (Full disclosure: both the above R pakages are developed by Rsquared Academy.).

diff uses certain special symbols and gives instructions to make the files identical. The instructions are on how to change the first file to make it identical to the second file. We list the symbols below

We will use the -w option to ignore white spaces while comparing the files.

diff -w imports_olsrr.txt imports_blorr.txt

## 1a2 ## > caret ## 3d3 ## < cli ## 4a5 ## >cli

Let us interpret the results. 4a5 indicates after line 4 in file 1, add line 5 from file 2 to make both the files identical i.e. add caret which is line 5 in imports_blorr.txt after line 4 in imports_olsrr.txt which will make both the files identical.

Let us change the file order and see the instructions from diff .

diff -w imports_blorr.txt imports_olsrr.txt

## 2d1 ## < caret ## 4d2 ## < clisymbols ## 5a4 ## >clisymbols

5d4 indicates delete line 5 from file 1 to match both the files at line4 i.e. delete caret which is line 5 in imports_blorr.txt to make both the files identical.

Side By Side

To view the differences between the files side by side, use the -y option.

diff -y imports_olsrr.txt imports_blorr.txt

## car | car ## checkmate | caret ## cli | checkmate ## clisymbols | clisymbols ## > cli

Unified Format

To view the differences between the files in a unified format, use the -u option.

diff -u imports_olsrr.txt imports_blorr.txt

## --- imports_olsrr.txt 2019-09-20 13:36:03.000000000 +0530 ## +++ imports_blorr.txt 2019-09-20 13:36:35.000000000 +0530 ## @@ -1,4 +1,5 @@ ## -car ## -checkmate ## -cli ## -clisymbols ## +car ## +caret ## +checkmate ## +clisymbols ## +cli

Compare Recursively

To compare recursively, use the -r option. Let us compare the mypackage and myproject folders.

diff -r mypackage myproject

## Only in mypackage: .Rbuildignore ## Only in mypackage: DESCRIPTION ## Only in mypackage: LICENSE ## Only in mypackage: NAMESPACE ## Only in mypackage: NEWS.md ## Only in mypackage: R ## Only in myproject/data: processed ## Only in myproject/data: raw ## Only in mypackage: docs ## Only in mypackage: man ## Only in myproject: output ## Only in myproject: run_analysis.R ## Only in mypackage: tests ## Only in mypackage: vignettes

File Details

To compare directories and view the names of files that differ, use the -rq option. In the below example, we look at the names of files that differ in mypackage and myproject folders.

diff -rq mypackage myproject

## Only in mypackage: .Rbuildignore ## Only in mypackage: DESCRIPTION ## Only in mypackage: LICENSE ## Only in mypackage: NAMESPACE ## Only in mypackage: NEWS.md ## Only in mypackage: R ## Only in myproject/data: processed ## Only in myproject/data: raw ## Only in mypackage: docs ## Only in mypackage: man ## Only in myproject: output ## Only in myproject: run_analysis.R ## Only in mypackage: tests ## Only in mypackage: vignettes

R Functions

In R, file operations can be performed using functions from both base R and the fs package.

Input/Output

In this section, we will explore commands that will

• display messages
• print file contents
• sort file contents

Display Messages

The echo command prints text to the terminal. It can be used for writing or appending messages to a file as well.

Print Message

Let us start with a simple example. We will print the text Action of the Toes to the terminal. It is the release name for R version 3.6.1.

echo Action of the Toes

Redirect Output

What if we want to redirect the output? Instead of printing the text to the terminal, we want to write it to a file. In such cases, use > along with the file name to redirect the output to the file. Keep in mind that > will overwrite files. If you want to append to files instead of overwriting, use >> .

echo Great Truth > release.txt

Print & Concatenate Files

The cat command reads data from files, and outputs their contents. It is the simplest way to display the contents of a file at the command line. It can be used to overwrite or append new content to files as well. cat stands for catenate and can be used to

• display text files
• copy text files into a new document
• append the contents of a text file to the end of another text file, combining them

Print Content

Let us print the content of the release_names.txt file (it contains R release names).

cat release_names.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle ## Roasted Marshmallows ## Trick or Treat ## Security Blanket ## Masked Marvel ## Good Sport ## Frisbee Sailing ## Warm Puppy ## Spring Dance ## Sock it to Me ## Pumpkin Helmet ## Smooth Sidewalk ## Full of Ingredients ## World-Famous Astronaut ## Fire Safety ## Wooden Christmas Tree ## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch ## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tree

Number All Output Lines

If you want to number the output line, use the -n option.

cat -n release_names.txt

## 1 Unsuffered Consequences ## 2 Great Pumpkin ## 3 December Snowflakes ## 4 Gift-Getting Season ## 5 Easter Beagle ## 6 Roasted Marshmallows ## 7 Trick or Treat ## 8 Security Blanket ## 9 Masked Marvel ## 10 Good Sport ## 11 Frisbee Sailing ## 12 Warm Puppy ## 13 Spring Dance ## 14 Sock it to Me ## 15 Pumpkin Helmet ## 16 Smooth Sidewalk ## 17 Full of Ingredients ## 18 World-Famous Astronaut ## 19 Fire Safety ## 20 Wooden Christmas Tree ## 21 Very Secure Dishes ## 22 Very, Very Secure Dishes ## 23 Supposedly Educational ## 24 Bug in Your Hair ## 25 Sincere Pumpkin Patch ## 26 Another Canoe ## 27 You Stupid Darkness ## 28 Single Candle ## 29 Short Summer ## 30 Kite Eating Tree

Concatenate Several Files

To concatenate the contents of several files into a target file, use > . In the below example, we concatenate the contents of the files release_names_18.txt and release_names_19.txt into a single file release_names_18_19.txt . In this case we are not printing the contents of the file to the terminal and instead we concatenate the contents from both the files and redirect the output to the target file.

cat release_names_18.txt release_names_19.txt > release_names_18_19.txt cat release_names_18_19.txt

## Someone to Lean On ## Joy in Playing ## Feather Spray ## Eggshell IglooGreat Truth ## Planting of a Tree ## Action of the Toes

Head

The head command will display the firt 10 lines of a file(s) by default. It can be used to display the first few lines or bytes of a file as well.

Output the first parts of a file

Let us use head to display the first 10 lines of the release_names.txt file.

head release_names.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle ## Roasted Marshmallows ## Trick or Treat ## Security Blanket ## Masked Marvel ## Good Sport

Output the first n lines of a file

Using the n option, we can specify the number of lines to be displayed. In the below example, we display the first 5 lines.

head -n 5 release_names.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle

Output the first c bytes of a file

The c option can be used to display characters or bytes instead of lines. Let us display the first 5 bytes of the release_names.txt file.

head -c 5 release_names.txt

## Unsuf

Output everything but the last 5 lines of a file

To display the last parts of a file, use - while specifying the number of lines. In the below example, we display the last 5 lines of the file.

head -n -5 release_names.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle ## Roasted Marshmallows ## Trick or Treat ## Security Blanket ## Masked Marvel ## Good Sport ## Frisbee Sailing ## Warm Puppy ## Spring Dance ## Sock it to Me ## Pumpkin Helmet ## Smooth Sidewalk ## Full of Ingredients ## World-Famous Astronaut ## Fire Safety ## Wooden Christmas Tree ## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch

Output everything but the last 3 bytes of a file

In this example, we display the last 3 bytes of the file using the c option and - while specifying the number of bytes.

head -c -3 release_names.txt

## Unsuffered Consequences ## Great Pumpkin ## December Snowflakes ## Gift-Getting Season ## Easter Beagle ## Roasted Marshmallows ## Trick or Treat ## Security Blanket ## Masked Marvel ## Good Sport ## Frisbee Sailing ## Warm Puppy ## Spring Dance ## Sock it to Me ## Pumpkin Helmet ## Smooth Sidewalk ## Full of Ingredients ## World-Famous Astronaut ## Fire Safety ## Wooden Christmas Tree ## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch ## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tre

Tail

The tail command displays the last 10 lines of a file(s) by default. It can be used to display the last few lines or bytes of a file as well.

Display the last parts of a file

Let us use tail to display the last 10 lines of the file.

tail release_names.txt

## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch ## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tree

Display the last 5 lines of a file

As we did in the previous section, use n to specify the number of lines to be displayed.

tail -n 5 release_names.txt

## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tree

Display all contents from line 10

We can use tail to display all contents of a file starting from a specific line. In the below example, we display all contents of the file starting from the 10th line using the n option and + prefix while specifying the number of lines.

tail -n +10 release_names.txt

## Good Sport ## Frisbee Sailing ## Warm Puppy ## Spring Dance ## Sock it to Me ## Pumpkin Helmet ## Smooth Sidewalk ## Full of Ingredients ## World-Famous Astronaut ## Fire Safety ## Wooden Christmas Tree ## Very Secure Dishes ## Very, Very Secure Dishes ## Supposedly Educational ## Bug in Your Hair ## Sincere Pumpkin Patch ## Another Canoe ## You Stupid Darkness ## Single Candle ## Short Summer ## Kite Eating Tree

Display the last 10 bytes of a file

Use the c option to display the last 7 bytes of a file.

tail -c 7 release_names.txt

## Tree

More

The more command displays text, one screen at a time. It opens a file for

• interactive reading
• scrolling
• and searching

Press space to scroll down the page, the forward slash ( / ) for searching strings, n to go to the next match and q to quit.

Less

The less command is similar to more but offers more features. It allows the user to scroll up and down, go to the beggining and end of the file, forward and backward search and the ability to go the next and previous match while searching the file.

Sort

The sort command will sort the contents of text file, line by line. Using additional options, we can

• sort a file in ascending/descending order
• ignore case while sorting
• use numeric order for sorting
• preserve only unique lines while sorting

Using the sort command, the contents can be sorted numerically and alphabetically. By default, the rules for sorting are:

• lines starting with a number will appear before lines starting with a letter.
• lines starting with a letter that appears earlier in the alphabet will appear before lines starting with a letter that appears later in the alphabet.
• lines starting with a lowercase letter will appear before lines starting with the same letter in uppercase.

Using additional options, the rules for sorting can be changed. We list the options in the below table.

Sort

Let us sort the contents of the pkg_names.txt file. It contains names R packages randomly selected from CRAN.

sort pkg_names.txt

## ASIP ## AdMit ## AnalyzeTS ## AzureStor ## AzureStor ## BIGDAWG ## BIOMASS ## BIOMASS ## BenfordTests ## BinOrdNonNor ## BioCircos ## ClimMobTools ## CombinePValue ## Eagle ## FField ## ICAOD ## MARSS ## MIAmaxent ## MIAmaxent ## MIAmaxent ## MVB ## MVTests ## MaXact ## MaxentVariableSelection ## OptimaRegion ## OxyBS ## PathSelectMP ## PropScrRand ## RJDBC ## RPyGeo ## SCRT ## SMARTp ## SPEDInstabR ## SemiParSampleSel ## SetMethods ## SmallCountRounding ## SpatioTemporal ## SphericalK ## SuppDists ## Survgini ## TIMP ## TSeriesMMA ## VineCopula ## WGScan ## WPKDE ## accept ## accept ## addhaz ## alfr ## aweek ## aweek ## bayesbio ## blink ## breakfast ## cbsem ## corclass ## crsra ## cyclocomp ## dagitty ## disparityfilter ## edfReader ## errorlocate ## expstudies ## fermicatsR ## foretell ## gLRTH ## gazepath ## generalhoslem ## geoknife ## hdnom ## hindexcalculator ## ibd ## interplot ## kfigr ## logNormReg ## ltxsparklines ## lue ## mbir ## mcmcabn ## mev ## mgcViz ## mined ## mlflow ## mongolite ## mongolite ## mvShapiroTest ## odk ## overlapping ## pAnalysis ## pls ## pmdplyr ## poisbinom ## randtests ## redcapAPI ## rgw ## rless ## rsed ## rstudioapi ## solitude ## splithalfr ## sspline ## sybilccFBA ## tailr ## tailr ## tictactoe ## viridisLite ## vqtl ## widyr ## widyr

Descending Order

Using the -r option which stands for --reverse the contents of the file can be sorted in descending/reverse order. Let us now sort the contents of the pkg_names.txt file in reverse order.

sort -r pkg_names.txt

## widyr ## widyr ## vqtl ## viridisLite ## tictactoe ## tailr ## tailr ## sybilccFBA ## sspline ## splithalfr ## solitude ## rstudioapi ## rsed ## rless ## rgw ## redcapAPI ## randtests ## poisbinom ## pmdplyr ## pls ## pAnalysis ## overlapping ## odk ## mvShapiroTest ## mongolite ## mongolite ## mlflow ## mined ## mgcViz ## mev ## mcmcabn ## mbir ## lue ## ltxsparklines ## logNormReg ## kfigr ## interplot ## ibd ## hindexcalculator ## hdnom ## geoknife ## generalhoslem ## gazepath ## gLRTH ## foretell ## fermicatsR ## expstudies ## errorlocate ## edfReader ## disparityfilter ## dagitty ## cyclocomp ## crsra ## corclass ## cbsem ## breakfast ## blink ## bayesbio ## aweek ## aweek ## alfr ## addhaz ## accept ## accept ## WPKDE ## WGScan ## VineCopula ## TSeriesMMA ## TIMP ## Survgini ## SuppDists ## SphericalK ## SpatioTemporal ## SmallCountRounding ## SetMethods ## SemiParSampleSel ## SPEDInstabR ## SMARTp ## SCRT ## RPyGeo ## RJDBC ## PropScrRand ## PathSelectMP ## OxyBS ## OptimaRegion ## MaxentVariableSelection ## MaXact ## MVTests ## MVB ## MIAmaxent ## MIAmaxent ## MIAmaxent ## MARSS ## ICAOD ## FField ## Eagle ## CombinePValue ## ClimMobTools ## BioCircos ## BinOrdNonNor ## BenfordTests ## BIOMASS ## BIOMASS ## BIGDAWG ## AzureStor ## AzureStor ## AnalyzeTS ## AdMit ## ASIP

Ignore case

To ignore case while sorting contents, use the --ignore-case option. Time to sort the pkg_names.txt file while ignoring case.

sort --ignore-case pkg_names.txt

## accept ## accept ## addhaz ## AdMit ## alfr ## AnalyzeTS ## ASIP ## aweek ## aweek ## AzureStor ## AzureStor ## bayesbio ## BenfordTests ## BIGDAWG ## BinOrdNonNor ## BioCircos ## BIOMASS ## BIOMASS ## blink ## breakfast ## cbsem ## ClimMobTools ## CombinePValue ## corclass ## crsra ## cyclocomp ## dagitty ## disparityfilter ## Eagle ## edfReader ## errorlocate ## expstudies ## fermicatsR ## FField ## foretell ## gazepath ## generalhoslem ## geoknife ## gLRTH ## hdnom ## hindexcalculator ## ibd ## ICAOD ## interplot ## kfigr ## logNormReg ## ltxsparklines ## lue ## MARSS ## MaXact ## MaxentVariableSelection ## mbir ## mcmcabn ## mev ## mgcViz ## MIAmaxent ## MIAmaxent ## MIAmaxent ## mined ## mlflow ## mongolite ## mongolite ## MVB ## mvShapiroTest ## MVTests ## odk ## OptimaRegion ## overlapping ## OxyBS ## pAnalysis ## PathSelectMP ## pls ## pmdplyr ## poisbinom ## PropScrRand ## randtests ## redcapAPI ## rgw ## RJDBC ## rless ## RPyGeo ## rsed ## rstudioapi ## SCRT ## SemiParSampleSel ## SetMethods ## SmallCountRounding ## SMARTp ## solitude ## SpatioTemporal ## SPEDInstabR ## SphericalK ## splithalfr ## sspline ## SuppDists ## Survgini ## sybilccFBA ## tailr ## tailr ## tictactoe ## TIMP ## TSeriesMMA ## VineCopula ## viridisLite ## vqtl ## WGScan ## widyr ## widyr ## WPKDE

Numeric Order

To sort numerically, use the -n option which stands for --numeric-sort . In this example, we will use a different file, package_names.txt where the package names are prefixed by random numbers between 1 and 100.

sort -n package_names.txt

## 1. cyclocomp ## 2. odk ## 3. redcapAPI ## 4. TIMP ## 5. pls ## 6. BinOrdNonNor ## 7. bayesbio ## 8. MVTests ## 9. pAnalysis ## 10. aweek ## 11. hdnom ## 12. ltxsparklines ## 13. MaXact ## 14. RJDBC ## 15. MIAmaxent ## 16. randtests ## 17. ASIP ## 18. gazepath ## 19. mcmcabn ## 20. rless ## 21. corclass ## 22. vqtl ## 23. disparityfilter ## 24. SCRT ## 25. RPyGeo ## 26. blink ## 27. gLRTH ## 28. splithalfr ## 29. sspline ## 29. sspline ## 30. logNormReg ## 31. BIGDAWG ## 31. BIGDAWG ## 32. SPEDInstabR ## 33. tailr ## 33. tailr ## 34. ibd ## 35. fermicatsR ## 36. mlflow ## 37. CombinePValue ## 38. BenfordTests ## 39. mev ## 40. MaxentVariableSelection ## 41. rstudioapi ## 42. OptimaRegion ## 43. accept ## 44. expstudies ## 45. solitude ## 45. solitude ## 46. cbsem ## 47. SMARTp ## 48. geoknife ## 49. SemiParSampleSel ## 50. mbir ## 51. interplot ## 52. ClimMobTools ## 53. MVB ## 54. OxyBS ## 55. hindexcalculator ## 56. MARSS ## 57. generalhoslem ## 58. alfr ## 59. AdMit ## 60. Eagle ## 61. PropScrRand ## 62. lue ## 63. dagitty ## 64. viridisLite ## 65. mined ## 65. mined ## 66. SuppDists ## 67. tictactoe ## 68. AzureStor ## 68. AzureStor ## 69. FField ## 70. rsed ## 70. rsed ## 71. kfigr ## 72. overlapping ## 72. overlapping ## 73. VineCopula ## 74. crsra ## 75. pmdplyr ## 76. errorlocate ## 77. SetMethods ## 78. sybilccFBA ## 79. mvShapiroTest ## 80. SpatioTemporal ## 81. mgcViz ## 82. breakfast ## 83. WPKDE ## 84. BIOMASS ## 85. edfReader ## 86. mongolite ## 87. WGScan ## 88. SphericalK ## 89. foretell ## 90. widyr ## 91. rgw ## 92. BioCircos ## 93. PathSelectMP ## 94. ICAOD ## 95. TSeriesMMA ## 96. poisbinom ## 97. AnalyzeTS ## 98. SmallCountRounding ## 99. Survgini ## 100. addhaz

Preserve Only Unique Lines

The -u option which stands for --unique will preserve only unique lines while sorting the contents of the file. In the below example, we remove all duplicate lines from the pkg_names.txt while sorting.

sort -u pkg_names.txt

## ASIP ## AdMit ## AnalyzeTS ## AzureStor ## BIGDAWG ## BIOMASS ## BenfordTests ## BinOrdNonNor ## BioCircos ## ClimMobTools ## CombinePValue ## Eagle ## FField ## ICAOD ## MARSS ## MIAmaxent ## MVB ## MVTests ## MaXact ## MaxentVariableSelection ## OptimaRegion ## OxyBS ## PathSelectMP ## PropScrRand ## RJDBC ## RPyGeo ## SCRT ## SMARTp ## SPEDInstabR ## SemiParSampleSel ## SetMethods ## SmallCountRounding ## SpatioTemporal ## SphericalK ## SuppDists ## Survgini ## TIMP ## TSeriesMMA ## VineCopula ## WGScan ## WPKDE ## accept ## accept ## addhaz ## alfr ## aweek ## bayesbio ## blink ## breakfast ## cbsem ## corclass ## crsra ## cyclocomp ## dagitty ## disparityfilter ## edfReader ## errorlocate ## expstudies ## fermicatsR ## foretell ## gLRTH ## gazepath ## generalhoslem ## geoknife ## hdnom ## hindexcalculator ## ibd ## interplot ## kfigr ## logNormReg ## ltxsparklines ## lue ## mbir ## mcmcabn ## mev ## mgcViz ## mined ## mlflow ## mongolite ## mvShapiroTest ## odk ## overlapping ## pAnalysis ## pls ## pmdplyr ## poisbinom ## randtests ## redcapAPI ## rgw ## rless ## rsed ## rstudioapi ## solitude ## splithalfr ## sspline ## sybilccFBA ## tailr ## tictactoe ## viridisLite ## vqtl ## widyr

Word Count

wc will print newline, word, and byte counts for file(s). If more than one file is specified, it will also print total line.

Count words, bytes and lines

wc release_names.txt

## 30 73 546 release_names.txt

Count lines in a file

wc -l release_names.txt

## 30 release_names.txt

Count words in a file

wc -w release_names.txt

## 73 release_names.txt

Count characters(bytes) in a file

wc -c release_names.txt

## 546 release_names.txt

Search & Regular Expressions

In this section, we will explore commands that will

• search for a given string in a file
• find files using names
• and search for binary executable files

grep

The grep command is used for pattern matching. Along with additional options, it can be used to

• match pattern in input text
• ignore case
• search recursively for an exact string
• print filename and line number for each match
• invert match for excluding specific strings

grep processes text line by line, and prints any lines which match a specified pattern. grep , which stands for global regular expression print is a powerful tool for matching a regular expression against text in a file, multiple files, or a stream of input.

Match Pattern in Input Text

Using grep let us search for packages that inlcude the letter R in their names.

grep R package_names.txt

## 14. RJDBC ## 30. logNormReg ## 27. gLRTH ## 35. fermicatsR ## 42. OptimaRegion ## 61. PropScrRand ## 25. RPyGeo ## 47. SMARTp ## 24. SCRT ## 56. MARSS ## 85. edfReader ## 32. SPEDInstabR ## 98. SmallCountRounding

Ignore Case

In the previous case, grep returned only those packages whose name included R but not r i.e. it did not ignore the case of the letter. Using the -i option, we will now search while ignoring the case of the letter.

grep -i R package_names.txt

## 14. RJDBC ## 58. alfr ## 64. viridisLite ## 99. Survgini ## 30. logNormReg ## 27. gLRTH ## 71. kfigr ## 72. overlapping ## 90. widyr ## 33. tailr ## 40. MaxentVariableSelection ## 33. tailr ## 72. overlapping ## 16. randtests ## 12. ltxsparklines ## 91. rgw ## 35. fermicatsR ## 21. corclass ## 68. AzureStor ## 42. OptimaRegion ## 61. PropScrRand ## 74. crsra ## 80. SpatioTemporal ## 23. disparityfilter ## 49. SemiParSampleSel ## 76. errorlocate ## 88. SphericalK ## 28. splithalfr ## 89. foretell ## 25. RPyGeo ## 50. mbir ## 51. interplot ## 6. BinOrdNonNor ## 47. SMARTp ## 38. BenfordTests ## 79. mvShapiroTest ## 92. BioCircos ## 55. hindexcalculator ## 41. rstudioapi ## 57. generalhoslem ## 24. SCRT ## 95. TSeriesMMA ## 82. breakfast ## 56. MARSS ## 70. rsed ## 68. AzureStor ## 85. edfReader ## 20. rless ## 75. pmdplyr ## 32. SPEDInstabR ## 3. redcapAPI ## 70. rsed ## 98. SmallCountRounding

Highlight

The --color option will highlight the matched strings.

grep -i --color R package_names.txt

## 14. RJDBC ## 58. alfr ## 64. viridisLite ## 99. Survgini ## 30. logNormReg ## 27. gLRTH ## 71. kfigr ## 72. overlapping ## 90. widyr ## 33. tailr ## 40. MaxentVariableSelection ## 33. tailr ## 72. overlapping ## 16. randtests ## 12. ltxsparklines ## 91. rgw ## 35. fermicatsR ## 21. corclass ## 68. AzureStor ## 42. OptimaRegion ## 61. PropScrRand ## 74. crsra ## 80. SpatioTemporal ## 23. disparityfilter ## 49. SemiParSampleSel ## 76. errorlocate ## 88. SphericalK ## 28. splithalfr ## 89. foretell ## 25. RPyGeo ## 50. mbir ## 51. interplot ## 6. BinOrdNonNor ## 47. SMARTp ## 38. BenfordTests ## 79. mvShapiroTest ## 92. BioCircos ## 55. hindexcalculator ## 41. rstudioapi ## 57. generalhoslem ## 24. SCRT ## 95. TSeriesMMA ## 82. breakfast ## 56. MARSS ## 70. rsed ## 68. AzureStor ## 85. edfReader ## 20. rless ## 75. pmdplyr ## 32. SPEDInstabR ## 3. redcapAPI ## 70. rsed ## 98. SmallCountRounding

Print Filename

If there is more than one file to search, use the -H option to print the filename for each match.

grep -i --color -H bio package_names.txt

## package_names.txt:84. BIOMASS ## package_names.txt:92. BioCircos ## package_names.txt:7. bayesbio

Print Corresponding Line Number

The -n option will print the corresponding line number of the match in the file.

grep -i --color -n bio package_names.txt

## 59:84. BIOMASS ## 71:92. BioCircos ## 88:7. bayesbio

Print Filename & Line Number

Let us print both the file name and the line number for each match.

grep -i --color -Hn R package_names.txt

## package_names.txt:1:14. RJDBC ## package_names.txt:3:58. alfr ## package_names.txt:8:64. viridisLite ## package_names.txt:14:99. Survgini ## package_names.txt:15:30. logNormReg ## package_names.txt:16:27. gLRTH ## package_names.txt:18:71. kfigr ## package_names.txt:20:72. overlapping ## package_names.txt:21:90. widyr ## package_names.txt:22:33. tailr ## package_names.txt:23:40. MaxentVariableSelection ## package_names.txt:26:33. tailr ## package_names.txt:27:72. overlapping ## package_names.txt:30:16. randtests ## package_names.txt:31:12. ltxsparklines ## package_names.txt:32:91. rgw ## package_names.txt:33:35. fermicatsR ## package_names.txt:37:21. corclass ## package_names.txt:38:68. AzureStor ## package_names.txt:41:42. OptimaRegion ## package_names.txt:42:61. PropScrRand ## package_names.txt:43:74. crsra ## package_names.txt:51:80. SpatioTemporal ## package_names.txt:52:23. disparityfilter ## package_names.txt:54:49. SemiParSampleSel ## package_names.txt:55:76. errorlocate ## package_names.txt:57:88. SphericalK ## package_names.txt:61:28. splithalfr ## package_names.txt:62:89. foretell ## package_names.txt:63:25. RPyGeo ## package_names.txt:64:50. mbir ## package_names.txt:65:51. interplot ## package_names.txt:66:6. BinOrdNonNor ## package_names.txt:67:47. SMARTp ## package_names.txt:68:38. BenfordTests ## package_names.txt:69:79. mvShapiroTest ## package_names.txt:71:92. BioCircos ## package_names.txt:75:55. hindexcalculator ## package_names.txt:78:41. rstudioapi ## package_names.txt:80:57. generalhoslem ## package_names.txt:84:24. SCRT ## package_names.txt:85:95. TSeriesMMA ## package_names.txt:87:82. breakfast ## package_names.txt:96:56. MARSS ## package_names.txt:97:70. rsed ## package_names.txt:98:68. AzureStor ## package_names.txt:100:85. edfReader ## package_names.txt:101:20. rless ## package_names.txt:102:75. pmdplyr ## package_names.txt:103:32. SPEDInstabR ## package_names.txt:104:3. redcapAPI ## package_names.txt:106:70. rsed ## package_names.txt:107:98. SmallCountRounding

Invert Match

Use the -v option to select non-matching lines. In the below example, we search for packages whose name does not include R while ignoring the case.

grep -v -i R package_names.txt

## 36. mlflow ## 10. aweek ## 31. BIGDAWG ## 22. vqtl ## 29. sspline ## 39. mev ## 66. SuppDists ## 15. MIAmaxent ## 31. BIGDAWG ## 29. sspline ## 60. Eagle ## 83. WPKDE ## 11. hdnom ## 26. blink ## 18. gazepath ## 52. ClimMobTools ## 44. expstudies ## 65. mined ## 81. mgcViz ## 45. solitude ## 9. pAnalysis ## 65. mined ## 94. ICAOD ## 48. geoknife ## 45. solitude ## 67. tictactoe ## 46. cbsem ## 93. PathSelectMP ## 96. poisbinom ## 17. ASIP ## 5. pls ## 84. BIOMASS ## 59. AdMit ## 77. SetMethods ## 53. MVB ## 2. odk ## 86. mongolite ## 4. TIMP ## 97. AnalyzeTS ## 87. WGScan ## 63. dagitty ## 69. FField ## 13. MaXact ## 73. VineCopula ## 7. bayesbio ## 34. ibd ## 8. MVTests ## 19. mcmcabn ## 43. accept ## 78. sybilccFBA ## 62. lue ## 100. addhaz ## 37. CombinePValue ## 1. cyclocomp ## 54. OxyBS

Recursive Search

Use the -r option to search recursively. In the below example, we search all files with the .txt extension for the string bio while ignoring the case.

grep -i --color -r bio *.txt

## package_names.txt:84. BIOMASS ## package_names.txt:92. BioCircos ## package_names.txt:7. bayesbio ## pkg_names.txt:BIOMASS ## pkg_names.txt:BioCircos ## pkg_names.txt:BIOMASS ## pkg_names.txt:bayesbio

find

The find command can be used for searching files and directories. Using additional options, we can

• search files by extension type
• ignore case while searching files/directories

find is a powerful tool for working with the files. It can be used on its own to locate files, or in conjunction with other programs to perform operations on those files.

Search Recursively

Let us use find to search for the file release_names.txt recursively. The -name option is used to specify the name of the file we are searching.

find -name release_names.txt

## ./release_names.txt ## ./r_releases/release_names.txt

There are two files with the name release_names.txt present in the current working directory and in r_releases directory.

Search by Extension

Let us search for all files with .txt extension in the r_releases folder.

find r_releases -name '*.txt'

## r_releases/release_names.txt ## r_releases/release_names_2.txt ## r_releases/release_names_3.txt

There are 3 files with the .txt extension in r_releases folder.

Case-insensitive Mode

Search for all folders with the name R or r . Here we use the -iname option to ignore case while searching. The -type option is used to specify whether we are searching for files or folders. Since we are searching for folder/directory, we use it along with d i.e. directory to indicate that we are searching for directories and not files.

find -type d -iname R

## ./mypackage/R ## ./r

Case-sensitive Mode

Search for all folders with the name r . It should exclude any folder with the name R .

find -type d -name r

Data Transfer & Network

In this section, we will explore commands that will allow us to download files from the internet.

We have not executed the commands in this ebook as downloading multiple files from the internet will take a lot of time or result in errors but we have checked all the commands offline to ensure that they work.

wget

The wget command will download contents of a URL and files from the internet. Using additional options, we can

• download contents/files to a file
• continue incomplete downloads
• download multiple files
• limit download speed and number of retries

Download URL

Let us first use wget to download contents of a URL. Note, we are not downloading file as such but just the content of the URL. We will use the URL of the home page of R project.

wget https://www.r-project.org/

If you look at the list of files, you can see a new file, index.html which we just downloaded using wget . Downloading contents this way will lead to confusion if we are dealing with multiple URLs. Let us learn to save the contents to a file (we can specify the name of the file which should help avoid confusion.)

Specify Filename

In this example, we download contents from the same URL and in addition specify the name of the file in which the content must be saved. Here we save it in a new file, rhomepage.html using the -o option followed by the filename.

wget -o rhomepage.html https://www.r-project.org/

Download File

How about downloading a file instead of a URL? In this example, we will download a logfile from the RStudio CRAN mirror. It contains the details of R downloads and individual package downloads. If you are a package developer and would want to know the countries in which your packages are downloaded, you will find this useful. We will download the file for 29th September and save it as sep_29.csv.gz .

wget -o sep_29.csv.gz http://cran-logs.rstudio.com/2019/2019-09-29.csv.gz

Download Multiple URLs

How do we download multiple URLs? One way is to specify the URLs one after the other separated by a space or save all URLs in a file and read them one by one. In the below example, we have saved multiple URLs in the file urls.txt .

cat urls.txt

## http://cran-logs.rstudio.com/2019/2019-09-26.csv.gz ## http://cran-logs.rstudio.com/2019/2019-09-27.csv.gz ## http://cran-logs.rstudio.com/2019/2019-09-28.csv.gz

We will download all the above URLs and save them in a new folder downloads . The -i indicates that the URLs must be read from a file (local or external). The -P option allows us to specify the directory into which all the files will be downloaded.

wget -P downloads -i urls.txt 

Quiet

The --quiet option will turn off wget output. It will not show any of the following details:

• name of the file being saved
• file size
• download speed
• eta etc.

wget –-quiet http://cran-logs.rstudio.com/2019/2019-10-06.csv.gz

No Verbose

Using the -nv or --no-verbose option, we can turn off verbose without being completely quiet (as we did in the previous example). Any error messages and basic information will still be printed.

wget –-no-verbose http://cran-logs.rstudio.com/2019/2019-10-13.csv.gz 

Check Timestamp

Let us say we have already downloaded a file from a URL. The file is updated from time to time and we intend to keep the local copy updated as well. Using the --timestamping option, the local file will have timestamp matching the remote file; if the remote file is not newer (not updated), no download will occur i.e. if the timestamp of the remote file has not changed it will not be downloaded. This is very useful in case of large files where you do not want to download them unless they have been updated.

wget –-timestamping http://cran-logs.rstudio.com/2019/2019-10-13.csv.gz

curl

The curl command will transfer data from or to a server. We will only look at downloading files from the internet.

Download URL

Let us download the home page of the R project using curl .

curl https://www.r-project.org/

Specify File

Let us download another log file from the RStudio CRAN mirror and save it into a file using the -o option.

curl http://cran-logs.rstudio.com/2019/2019-09-08.csv.gz -o sept_08.csv.gz 

Another way to save a downloaded file is to use > followed by the name of the file as shown in the below example.

curl http://cran-logs.rstudio.com/2019/2019-09-01.csv.gz > sep_01.csv.gz

Download Silently

The -s option will allow you to download files silently. It will mute curl and will not display progress meter or error messages.

curl http://cran-logs.rstudio.com/2019/2019-09-01.csv.gz -o sept_01.csv.gz -s

R Functions

In R, we can use download.file() to download files from the internet. The following packages offer functionalities that you will find useful.

sudo

sudo Super User DO is a prefix of commands that only superuser or root users are allowed to run. It is similar to run as administrator option in Windows. It is used to install, update and remove software. We will use it in the next section to install & update packages. If you are using RStudio Cloud, you will not be able to run sudo (users do not have root privileges).

File Compression

tar

The tar command is used for file compression. It works with both tar and tar.gz extensions. It is used to

• list files
• extract files
• create archives
• append file to existing archives

tar creates, maintains, modifies, and extracts files that are archived in the tar format. Tar stands for tape archive and is an archiving file format.

We will use different options along with the tar command for listing, extracting, creating and adding files. The vf (v stands for verbosely show .tar file progress and f stands for file name type of the archive file) option is common for all the above operations while the following are specific.

• t for listing
• x for extracting
• c for creating
• r for adding files

While dealing with tar.gz archives we will use z in addition to vf and the above options.

List

Let us list all the files & folders in release_names.tar . As mentioned above. to list the files in the archive, we use the t option.

tar -tvf release_names.tar 

## -rwxrwxrwx aravind/aravind 546 2019-09-16 15:59 release_names.txt ## -rwxrwxrwx aravind/aravind 65 2019-09-16 15:58 release_names_18.txt ## -rwxrwxrwx aravind/aravind 53 2019-09-16 15:59 release_names_19.txt

Extract

Let us extract files from release_names.tar using the x option in addition to vf .

tar -xvf release_names.tar ls

## release_names.txt ## release_names_18.txt ## release_names_19.txt ## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_18_19.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Add

To add a file to an existing archive, use the r option. Let us add release_names_18.txt and release_names_19.txt to the archive we created in the previous step.

tar -rvf release_names.tar release_names_18.txt release_names_19.txt

## release_names_18.txt ## release_names_19.txt

Create

Using the c option we can create tar archives. In the below example, we are using a single file but you can specify multiple files and folders as well.

tar -cvf pkg_names.tar pkg_names.txt

## pkg_names.txt

gzip

gzip , gunzip , and zcat commands are used to compress or expand files in the GNU GZIP format i.e. files with .gz extension

Compress

Let us compress release_names.txt file using gzip .

gzip release_names.txt ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.tar ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt.gz ## release_names_18.txt ## release_names_18_19.txt ## release_names_19.txt ## sept_15.csv.gz ## urls.txt ## zip_example.zip

Decompress

Use the -d option with gzip to decompress a file. In the below example, we decompress the sept_15.csv.gz file (downloaded using wget or curl earlier). You can also use gunzip for the same result.

gzip -d sept_15.csv.gz ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.tar ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_18_19.txt ## release_names_19.txt ## sept_15.csv ## urls.txt ## zip_example.zip

Specify Filename

Use -c and > to specify a different file name while compressing using gzip . In the below example, gzip will create releases.txt.gz instead of release_names.txt.gz .

gzip -c release_names.txt > releases.txt.gz ls

## analysis.R ## bash.R ## bash.sh ## imports_blorr.txt ## imports_olsrr.txt ## lorem-ipsum.txt ## main_project.zip ## myfiles ## mypackage ## myproject ## myproject3 ## myproject4 ## package_names.txt ## pkg_names.tar ## pkg_names.txt ## r ## r2 ## r_releases ## release_names.tar ## release_names.tar.gz ## release_names.txt ## release_names_18.txt ## release_names_18_19.txt ## release_names_19.txt ## releases.txt.gz ## sept_15.csv ## urls.txt ## zip_example.zip

zip & unzip

zip creates ZIP archives while unzip lists and extracts compressed files in a ZIP archive.

List

Let us list all the files and folders in main_project.zip() using unzip and the -l option.

unzip -l main_project.zip

## Archive: main_project.zip ## Length Date Time Name ## --------- ---------- ----- ---- ## 0 2019-09-23 18:07 myproject/ ## 0 2019-09-20 14:02 myproject/.gitignore ## 0 2019-09-23 18:07 myproject/data/ ## 0 2019-09-20 14:02 myproject/data/processed/ ## 0 2019-09-20 14:02 myproject/data/raw/ ## 0 2019-09-20 14:02 myproject/output/ ## 0 2019-09-20 14:02 myproject/README.md ## 13 2019-09-20 14:02 myproject/run_analysis.R ## 0 2019-09-20 14:02 myproject/src/ ## 0 2019-09-23 18:07 mypackage/ ## 0 2019-09-20 14:11 mypackage/.gitignore ## 0 2019-09-20 14:11 mypackage/.Rbuildignore ## 0 2019-09-20 14:10 mypackage/data/ ## 0 2019-09-20 14:11 mypackage/DESCRIPTION ## 0 2019-09-20 14:10 mypackage/docs/ ## 0 2019-09-20 14:11 mypackage/LICENSE ## 0 2019-09-20 14:10 mypackage/man/ ## 0 2019-09-20 14:11 mypackage/NAMESPACE ## 0 2019-09-20 14:11 mypackage/NEWS.md ## 0 2019-09-20 14:10 mypackage/R/ ## 0 2019-09-20 14:11 mypackage/README.md ## 0 2019-09-20 14:11 mypackage/src/ ## 0 2019-09-20 14:10 mypackage/tests/ ## 0 2019-09-20 14:10 mypackage/vignettes/ ## 0 2019-09-23 18:07 myfiles/ ## 12 2019-09-20 15:30 myfiles/analysis.R ## 7 2019-09-20 15:31 myfiles/NEWS.md ## 9 2019-09-20 15:31 myfiles/README.md ## 546 2019-09-20 15:29 myfiles/release_names.txt ## 65 2019-09-20 15:29 myfiles/release_names_18.txt ## 53 2019-09-20 15:30 myfiles/release_names_19.txt ## 12 2019-09-20 15:30 myfiles/visualization.R ## 15333 2019-10-01 16:58 bash.sh ## 0 2019-09-16 12:42 r/ ## --------- ------- ## 16050 34 files

Extract

Using unzip , let us now extract files and folders from zip_example.zip .

unzip zip_example.zip

## Archive: zip_example.zip ## creating: zip_example/ ## inflating: zip_example/bash.sh ## inflating: zip_example/pkg_names.txt

Using the -d option, we can extract the contents of zip_example.zip to a specific folder. In the below example, we extract it to a new folder examples .

unzip zip_example.zip –d myexamples

## [1] "Archive: zip_example.zip" ## [2] " creating: examples/zip_example/" ## [3] " inflating: examples/zip_example/bash.sh " ## [4] " inflating: examples/zip_example/pkg_names.txt "

Compress

Use the -r option along with zip to create a ZIP archive. In the below example, we create a ZIP archive of myproject folder.

zip -r myproject.zip myproject ls

## adding: myproject/ (stored 0%) ## adding: myproject/.gitignore (stored 0%) ## adding: myproject/data/ (stored 0%) ## adding: myproject/data/processed/ (stored 0%) ## adding: myproject/data/raw/ (stored 0%) ## adding: myproject/output/ (stored 0%) ## adding: myproject/README.md (stored 0%) ## adding: myproject/run_analysis.R (stored 0%) ## adding: myproject/src/ (stored 0%)

We can compress multiple directories using zip . The names of the directories must be separated by a space as shown in the below example where we compress myproject and mypackage into a single ZIP archive.

zip -r packproj.zip myproject mypackage ls

## adding: myproject/ (stored 0%) ## adding: myproject/.gitignore (stored 0%) ## adding: myproject/data/ (stored 0%) ## adding: myproject/data/processed/ (stored 0%) ## adding: myproject/data/raw/ (stored 0%) ## adding: myproject/output/ (stored 0%) ## adding: myproject/README.md (stored 0%) ## adding: myproject/run_analysis.R (stored 0%) ## adding: myproject/src/ (stored 0%) ## adding: mypackage/ (stored 0%) ## adding: mypackage/.gitignore (stored 0%) ## adding: mypackage/.Rbuildignore (stored 0%) ## adding: mypackage/data/ (stored 0%) ## adding: mypackage/DESCRIPTION (stored 0%) ## adding: mypackage/docs/ (stored 0%) ## adding: mypackage/LICENSE (stored 0%) ## adding: mypackage/man/ (stored 0%) ## adding: mypackage/NAMESPACE (stored 0%) ## adding: mypackage/NEWS.md (stored 0%) ## adding: mypackage/R/ (stored 0%) ## adding: mypackage/README.md (stored 0%) ## adding: mypackage/src/ (stored 0%) ## adding: mypackage/tests/ (stored 0%) ## adding: mypackage/vignettes/ (stored 0%)

Add

To add a new file/folder to an existing archive, specify the name of the archive followed by the name of the file or the folder. In the below example, we add the bash.sh file to the myproject.zip archive created in a previous step.

zip myproject.zip bash.sh

## adding: bash.sh (deflated 78%)

R Functions

tar & tar.gz

In R, we can use the tar() and untar() functions from the utils package to handle .tar and .tar.gz archives.

zip & gzip

The zip package has the functionalities to handle ZIP archives. The tar() and untar() functions from the utils package can handle GZIP archives.

System Info

In this section, we will explore commands that will allow us to

• display information about the system
• display memory usage information
• display file system disk space usage
• exit the terminal
• run commands a superuser
• shutdown the system

uname

The uname command is used to view important information about the system. Using additional options, we can

• print details about operating system
• hardware & software related information

Print all available information about the system

uname -a

## Linux Aravind 4.4.0-18362-Microsoft #836-Microsoft Mon May 05 16:04:00 PST 2020 x86_64 x86_64 x86_64 GNU/Linux

Display free, used, swap memory in the system

free

## total used free shared buff/cache available ## Mem: 3621900 1815864 1576684 17720 229352 1672304 ## Swap: 11010048 260640 10749408

Display file system disk space usage

## Filesystem 1K-blocks Used Available Use% Mounted on ## rootfs 188482144 142470276 46011868 76% / ## none 188482144 142470276 46011868 76% /dev ## none 188482144 142470276 46011868 76% /run ## none 188482144 142470276 46011868 76% /run/lock ## none 188482144 142470276 46011868 76% /run/shm ## none 188482144 142470276 46011868 76% /run/user ## cgroup 188482144 142470276 46011868 76% /sys/fs/cgroup ## C:\ 188482144 142470276 46011868 76% /mnt/c ## D:\ 18660348 17154308 1506040 92% /mnt/d ## F:\ 3196924 231756 2965168 8% /mnt/f ## G:\ 86383612 24561220 61822392 29% /mnt/g ## H:\ 86383612 14755988 71627624 18% /mnt/h ## J:\ 83185660 18797916 64387744 23% /mnt/j

Others

In this section, let us look at a few other useful commands that will allow us to

• see how long a command takes to execute
• delay activity
• display and clear command history list

Funny Commands

Below are a few funny commands for you to try out. Use sudo apt-get install to install fortune and banner before trying them.

R Functions

In R, we can use Sys.sleep() to delay activity and history() to view command history.

Execute Commands from R

Now, let us turn our attention to executing commands from R using system2() . Here we will focus on the following

• execute a command without arguments
• execute commands with arguments
• redirect output

Let us try to execute a command without any additional arguments. We will execute the ls command to list all files and directories. Use system2() and specify the command using the command argument. Whenever you are trying to execute a command from R, the first argument or input should be the command and it must be enclosed in quotes.

system2(command = "ls")

## [1] "2017-02-05-variables.Rmd" ## [2] "2017-02-05-variables.html" ## [3] "2017-02-17-data-types-in-r.Rmd" ## [4] "2017-02-17-data-types-in-r.html" ## [5] "2017-03-01-getting-help-in-r.html" ## [6] "2017-03-13-beginners-guide-to-r-package-ecosystem.Rmd" ## [7] "2017-03-13-beginners-guide-to-r-package-ecosystem.html" ## [8] "2017-03-25-vectors.Rmd" ## [9] "2017-03-25-vectors.html" ## [10] "2017-03-29-vectors-part-2.Rmd" ## [11] "2017-03-29-vectors-part-2.html" ## [12] "2017-04-03-vectors-part-3.Rmd" ## [13] "2017-04-03-vectors-part-3.html" ## [14] "2017-04-06-matrix.Rmd" ## [15] "2017-04-06-matrix.html" ## [16] "2017-04-12-matrix-part-2.Rmd" ## [17] "2017-04-12-matrix-part-2.html" ## [18] "2017-04-18-lists.Rmd" ## [19] "2017-04-18-lists.html" ## [20] "2017-04-30-factors.Rmd" ## [21] "2017-04-30-factors.html" ## [22] "2017-05-12-dataframes.Rmd" ## [23] "2017-05-12-dataframes.html" ## [24] "2017-05-24-data-visualization-with-r-introduction.Rmd" ## [25] "2017-05-24-data-visualization-with-r-introduction.html" ## [26] "2017-06-05-data-visualization-with-r-title-and-axis-labels.Rmd" ## [27] "2017-06-05-data-visualization-with-r-title-and-axis-labels.html" ## [28] "2017-06-17-data-visualization-with-r-scatter-plots.Rmd" ## [29] "2017-06-17-data-visualization-with-r-scatter-plots.html" ## [30] "2017-06-29-data-visualization-with-r-line-graphs.Rmd" ## [31] "2017-06-29-data-visualization-with-r-line-graphs.html" ## [32] "2017-07-11-data-visualization-with-r-bar-plots.Rmd" ## [33] "2017-07-11-data-visualization-with-r-bar-plots.html" ## [34] "2017-07-23-data-visualization-with-r-box-plots.Rmd" ## [35] "2017-07-23-data-visualization-with-r-box-plots.html" ## [36] "2017-08-04-data-visualization-with-r-histogram.Rmd" ## [37] "2017-08-04-data-visualization-with-r-histogram.html" ## [38] "2017-08-16-data-visualization-with-r-legends.Rmd" ## [39] "2017-08-16-data-visualization-with-r-legends.html" ## [40] "2017-08-28-data-visualization-with-r-text-annotations.Rmd" ## [41] "2017-08-28-data-visualization-with-r-text-annotations.html" ## [42] "2017-09-09-data-visualization-with-r-combining-plots.Rmd" ## [43] "2017-09-09-data-visualization-with-r-combining-plots.html" ## [44] "2017-10-03-ggplot2-quick-tour.Rmd" ## [45] "2017-10-03-ggplot2-quick-tour.html" ## [46] "2017-10-15-ggplot2-introduction-to-geoms.Rmd" ## [47] "2017-10-15-ggplot2-introduction-to-geoms.html" ## [48] "2017-10-27-ggplot2-introduction-to-aesthetics.Rmd" ## [49] "2017-10-27-ggplot2-introduction-to-aesthetics.html" ## [50] "2017-11-08-ggplot2-axis-plot-labels.Rmd" ## [51] "2017-11-08-ggplot2-axis-plot-labels.html" ## [52] "2017-11-20-ggplot2-text-annotations.Rmd" ## [53] "2017-11-20-ggplot2-text-annotations.html" ## [54] "2017-12-02-ggplot2-scatter-plots.Rmd" ## [55] "2017-12-02-ggplot2-scatter-plots.html" ## [56] "2017-12-14-ggplot2-line-graphs.Rmd" ## [57] "2017-12-14-ggplot2-line-graphs.html" ## [58] "2017-12-26-ggplot2-bar-plots.Rmd" ## [59] "2017-12-26-ggplot2-bar-plots.html" ## [60] "2018-01-07-ggplot2-box-plots.Rmd" ## [61] "2018-01-07-ggplot2-box-plots.html" ## [62] "2018-01-19-ggplot2-histogram.Rmd" ## [63] "2018-01-19-ggplot2-histogram.html" ## [64] "2018-01-31-ggplot2-guides-axes.Rmd" ## [65] "2018-01-31-ggplot2-guides-axes.html" ## [66] "2018-02-12-ggplot2-guides-legends.Rmd" ## [67] "2018-02-12-ggplot2-guides-legends.html" ## [68] "2018-02-24-guides-legends-part-2.Rmd" ## [69] "2018-02-24-guides-legends-part-2.html" ## [70] "2018-03-08-legend-part-3.Rmd" ## [71] "2018-03-08-legend-part-3.html" ## [72] "2018-03-20-legend-part-4.Rmd" ## [73] "2018-03-20-legend-part-4.html" ## [74] "2018-04-01-legend-part-5.Rmd" ## [75] "2018-04-01-legend-part-5.html" ## [76] "2018-04-13-legend-part-6.Rmd" ## [77] "2018-04-13-legend-part-6.html" ## [78] "2018-04-25-ggplot2-facets-combine-multiple-plots.Rmd" ## [79] "2018-04-25-ggplot2-facets-combine-multiple-plots.html" ## [80] "2018-05-07-ggplot2-themes.Rmd" ## [81] "2018-05-07-ggplot2-themes.html" ## [82] "2018-07-30-importing-data-into-r-part-1.Rmd" ## [83] "2018-07-30-importing-data-into-r-part-1.html" ## [84] "2018-08-11-importing-data-into-r-part-2.Rmd" ## [85] "2018-08-11-importing-data-into-r-part-2.html" ## [86] "2018-08-23-data-wrangling-with-dplyr-part-1.Rmd" ## [87] "2018-08-23-data-wrangling-with-dplyr-part-1.html" ## [88] "2018-09-04-data-wrangling-with-dplyr-part-2.Rmd" ## [89] "2018-09-04-data-wrangling-with-dplyr-part-2.html" ## [90] "2018-09-16-data-wrangling-with-dplyr-part-3.Rmd" ## [91] "2018-09-16-data-wrangling-with-dplyr-part-3.html" ## [92] "2018-09-28-introduction-to-tibbles.Rmd" ## [93] "2018-09-28-introduction-to-tibbles.html" ## [94] "2018-10-10-readable-code-with-pipes.Rmd" ## [95] "2018-10-10-readable-code-with-pipes.html" ## [96] "2018-10-22-hacking-strings-with-stringr.Rmd" ## [97] "2018-10-22-hacking-strings-with-stringr.html" ## [98] "2018-11-03-working-with-dates-in-r.Rmd" ## [99] "2018-11-03-working-with-dates-in-r.html" ## [100] "2018-11-15-working-with-categorical-data-using-forcats.Rmd" ## [101] "2018-11-15-working-with-categorical-data-using-forcats.html" ## [102] "2018-11-27-quick-guide-r-sqlite.Rmd" ## [103] "2018-11-27-quick-guide-r-sqlite.html" ## [104] "2018-12-09-data-wrangling-with-dbplyr.Rmd" ## [105] "2018-12-09-data-wrangling-with-dbplyr.html" ## [106] "2018-12-21-sql-for-data-science.Rmd" ## [107] "2018-12-21-sql-for-data-science.html" ## [108] "2019-01-02-sql-for-data-science-part-2.Rmd" ## [109] "2019-01-02-sql-for-data-science-part-2.html" ## [110] "2019-02-08-introducing-olsrr.Rmd" ## [111] "2019-02-08-introducing-olsrr.html" ## [112] "2019-02-12-introducing-rfm.Rmd" ## [113] "2019-02-12-introducing-rfm.html" ## [114] "2019-02-19-introducing-descriptr.Rmd" ## [115] "2019-02-19-introducing-descriptr.html" ## [116] "2019-02-20-introducing-descriptr.Rmd" ## [117] "2019-02-20-introducing-descriptr.html" ## [118] "2019-02-26-introducing-blorr.Rmd" ## [119] "2019-02-26-introducing-blorr.html" ## [120] "2019-03-05-getting-help-in-r.Rmd" ## [121] "2019-03-05-getting-help-in-r.html" ## [122] "2019-03-12-introducing-rbin.Rmd" ## [123] "2019-03-12-introducing-rbin.html" ## [124] "2019-03-14-introducing-vistributions.Rmd" ## [125] "2019-03-14-introducing-vistributions.html" ## [126] "2019-04-01-shiny-apps.Rmd" ## [127] "2019-04-01-shiny-apps.html" ## [128] "2019-04-11-web-scraping.Rmd" ## [129] "2019-04-11-web-scraping.html" ## [130] "2019-04-13-web-scraping-note.Rmd" ## [131] "2019-04-13-web-scraping-note.html" ## [132] "2019-05-02-mba.Rmd" ## [133] "2019-05-02-mba.html" ## [134] "2019-05-02-mba_files" ## [135] "2019-05-27-regex.Rmd" ## [136] "2019-05-27-regex.html" ## [137] "2019-07-05-pkginfo.Rmd" ## [138] "2019-07-05-pkginfo.html" ## [139] "2019-07-22-customer-segmentation-using-rfm-analysis.Rmd" ## [140] "2019-07-22-customer-segmentation-using-rfm-analysis.html" ## [141] "2019-07-22-customer-segmentation-using-rfm-analysis_files" ## [142] "2019-08-08-working-with-databases-using-r.Rmd" ## [143] "2019-08-08-working-with-databases-using-r.html" ## [144] "2019-08-08-working-with-databases-using-r_files" ## [145] "2019-10-26-command-line-crash-course.Rmd" ## [146] "2019-10-26-command-line-crash-course_files" ## [147] "2020-01-17-nse2r-intro.Rmd" ## [148] "2020-04-17-handling-date-and-time-in-r.Rmd" ## [149] "2020-04-17-handling-date-and-time-in-r_files" ## [150] "airline.dta" ## [151] "airline.sas7bdat" ## [152] "analysis.R" ## [153] "cline" ## [154] "config.yml" ## [155] "employee.sav" ## [156] "examples" ## [157] "hsb2.csv" ## [158] "hsb3.csv" ## [159] "hsb4.csv" ## [160] "imports_blorr.txt" ## [161] "imports_olsrr.txt" ## [162] "mydatabase.db" ## [163] "mypackage" ## [164] "myproject" ## [165] "online-retail.xlsx" ## [166] "options.R" ## [167] "package_names.csv" ## [168] "release.txt" ## [169] "sample.xls" ## [170] "transaction_data.csv" ## [171] "zip_example.zip"

Great! Now, how do we specify the options? The additional options of a command must be stored as a character vector and specified using the args argument. In the below example, we delete the examples folder we created earlier while decompressing the zip_example.zip file.

system2(command = "rm", args = c("-r", "examples"))

## character(0)

In some cases, we might want to redirect the output. Let us say we are writing message to a file using the echo command. In this cases, we want the output to be redirected to the release.txt file. The stdout argument can be used to redirect output to a file or the R console. In the below example, we redirect the output to a file.

system2(command = "echo", args = c("Great Truth"), stdout = "release.txt")

In the next example, we redirect the output to the R console by setting the value of the stdout argument to TRUE . If you are curious, set the value to FALSE and see what happens.

system2(command = "diff", args = c("imports_olsrr.txt", "imports_blorr.txt"), stdout = TRUE)

## Warning in system2(command = "diff", args = c("imports_olsrr.txt", ## "imports_blorr.txt"), : running command '"diff" imports_olsrr.txt ## imports_blorr.txt' had status 1

## [1] "1,4c1,5" " < car " "< checkmate" "< cli" "< clisymbols" ## [6] "---" ">car" "> caret" "> checkmate" "> clisymbols" ## [11] "> cli" ## attr(,"status") ## [1] 1

The run() command from the processx package can be used to execute shell commands as well.

Execute Shell Commands in RStudio

In RStudio, commands can be executed from shell scripts by pressing Ctrl + Enter . Instead of sending the command to the R console, it is redirected to the terminal where it is executed as shown below.

RMarkdown

RMarkdown supports bash , sh and awk . This post was initially created using sh as the underlying operating system is Windows. Later, we used bash after installing the Windows subsystem for Linux. Click here to learn more.

R in the Shell

In this section, we will learn to execute R commands and scripts in the command line using:

The -e option allows us to specify R expression(s). R -e will launch R and then execute the code specified within quotes. Use semi-colon to execute multiple expressions as shown below. You will be able to run the below commands only if you are able to launch R from the command line. Windows users need to ensure that R is added to the path environment.

R -e "head(mtcars); tail(mtcars)"

## ## R version 4.0.0 (2020-04-24) -- "Arbor Day" ## Copyright (C) 2020 The R Foundation for Statistical Computing ## Platform: x86_64-w64-mingw32/x64 (64-bit) ## ## R is free software and comes with ABSOLUTELY NO WARRANTY. ## You are welcome to redistribute it under certain conditions. ## Type 'license()' or 'licence()' for distribution details. ## ## Natural language support but running in an English locale ## ## R is a collaborative project with many contributors. ## Type 'contributors()' for more information and ## 'citation()' on how to cite R or R packages in publications. ## ## Type 'demo()' for some demos, 'help()' for on-line help, or ## 'help.start()' for an HTML browser interface to help. ## Type 'q()' to quit R. ## ## > head(mtcars); tail(mtcars) ## mpg cyl disp hp drat wt qsec vs am gear carb ## Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 ## Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 ## Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 ## Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 ## Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 ## Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1 ## mpg cyl disp hp drat wt qsec vs am gear carb ## Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.7 0 1 5 2 ## Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.9 1 1 5 2 ## Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.5 0 1 5 4 ## Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.5 0 1 5 6 ## Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.6 0 1 5 8 ## Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.6 1 1 4 2 ## > ## >

Rscript -e will run code without launching R.

Rscript -e "head(mtcars)"

## mpg cyl disp hp drat wt qsec vs am gear carb ## Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 ## Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 ## Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 ## Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 ## Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 ## Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1

We can use Rscript to execute a R script as well. In the below example, we execute the code in analysis.R file.

Rscript analysis.R

## mpg cyl disp hp drat wt qsec vs am gear carb ## Mazda RX4 21.0 6 160 110 3.90 2.620 16.46 0 1 4 4 ## Mazda RX4 Wag 21.0 6 160 110 3.90 2.875 17.02 0 1 4 4 ## Datsun 710 22.8 4 108 93 3.85 2.320 18.61 1 1 4 1 ## Hornet 4 Drive 21.4 6 258 110 3.08 3.215 19.44 1 0 3 1 ## Hornet Sportabout 18.7 8 360 175 3.15 3.440 17.02 0 0 3 2 ## Valiant 18.1 6 225 105 2.76 3.460 20.22 1 0 3 1

If you are more interested, try the littler package as well.

What we have not covered…

• shell scripting
• editing files
• file permissions
• user information
• pipes
• awk
• sed

Summary

• Shell is a text based application for viewing, handling and manipulating files
• It is also known by the following names
  • CLI (Command Line Inteface)
  • Terminal
  • Bash (Bourne Again Shell)

  References & Further Readings

  • https://tldr.sh/
  • https://blog.rstudio.com/2017/08/11/rstudio-v1-1-preview-terminal/
  • https://support.rstudio.com/hc/en-us/articles/115010737148-Using-the-RStudio-Terminal
  • https://bookdown.org/yihui/rmarkdown/language-engines.html#shell-scripts
  • https://github.com/kirillseva/tldrrr
  • https://fs.r-lib.org/articles/function-comparisons.html
  • https://livefreeordichotomize.com/2017/09/28/r-release-names/
  • https://stackoverflow.com/questions/13478375/is-there-any-authoritative-documentation-on-r-release-nicknames
  • http://www2.imm.dtu.dk/courses/02333/cygwin_tutorial/index.html
  • https://tutorial.djangogirls.org/en/intro_to_command_line/
  • https://ss64.com/
  • https://www.learnenough.com/command-line-tutorial

  Feedback

  If you see mistakes or want to suggest changes, please create an issue on the source repository or reach out to us at support@rsquaredacademy.com.

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